void checkPoints(size_t start, size_t end) const
{
float radius = 0.0f;
float distToBoundary = 0.0f;
int64_t numPoints = m_Points->getNumberOfVertices();
FloatArrayType::Pointer llPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Lower");
FloatArrayType::Pointer urPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Upper_Right");
float* ll = llPtr->getPointer(0);
float* ur = urPtr->getPointer(0);
float* point = NULL;
char code = ' ';
for (size_t iter = start; iter < end; iter++)
{
// find bounding box for current feature
GeometryMath::FindBoundingBoxOfFaces(m_Faces, m_FaceIds->getElementList(iter), ll, ur);
GeometryMath::FindDistanceBetweenPoints(ll, ur, radius);
// check points in vertex array to see if they are in the bounding box of the feature
for (int64_t i = 0; i < numPoints; i++)
{
point = m_Points->getVertexPointer(i);
if (m_PolyIds[i] == 0 && GeometryMath::PointInBox(point, ll, ur) == true)
{
code = GeometryMath::PointInPolyhedron(m_Faces, m_FaceIds->getElementList(iter), m_FaceBBs, point, ll, ur, radius, distToBoundary);
if (code == 'i' || code == 'V' || code == 'E' || code == 'F') { m_PolyIds[i] = iter; }
}
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
IGeometry::Pointer VertexGeom::deepCopy()
{
VertexGeom::Pointer vertexCopy = VertexGeom::CreateGeometry(getVertices(), getName());
vertexCopy->setSpatialDimensionality(getSpatialDimensionality());
return vertexCopy;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MakeDataContainer::dataCheck()
{
DataArrayPath tempPath;
setErrorCondition(0);
DataContainer::Pointer m = getDataContainerArray()->createNonPrereqDataContainer<AbstractFilter>(this, getDataContainerName());
if (getErrorCondition() < 0)
{
return;
}
QVector<size_t> tDims(3, 64);
AttributeMatrix::Pointer cellAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::Cell);
if (getErrorCondition() < 0)
{
return;
}
// tDims.resize(1);
// tDims[0] = 0;
// AttributeMatrix::Pointer cellEnsembleAttrMat = m->createNonPrereqAttributeMatrix<AbstractFilter>(this, getCellEnsembleAttributeMatrixName(), tDims, DREAM3D::AttributeMatrixType::CellEnsemble);
// if(getErrorCondition() < 0)
// {
// return;
// }
QVector<size_t> dims(1, 1);
m_FeatureIdsPtr = cellAttrMat->createNonPrereqArray<DataArray<int32_t>, AbstractFilter, int32_t>(this, m_FeatureIdsArrayName, 0, dims); /* Assigns the shared_ptr<> to an instance variable that is a weak_ptr<> */
if( NULL != m_FeatureIdsPtr.lock().get() ) /* Validate the Weak Pointer wraps a non-NULL pointer to a DataArray<T> object */
{
m_FeatureIds = m_FeatureIdsPtr.lock()->getPointer(0); /* Now assign the raw pointer to data from the DataArray<T> object */
}
//ImageGeom::Pointer image = ImageGeom::CreateGeometry("TestImageGeom");
//image->setResolution(0.1f, 0.2f, 0.3f);
//image->setOrigin(100.3f, 987.234f, 0.0f);
//image->setDimensions(64, 64, 64);
//m->setGeometry(image);
VertexGeom::Pointer vertices = VertexGeom::CreateGeometry(100, "TestVertexGeom");
SharedVertexList::Pointer test = vertices->getVertices();
float* verts = test->getPointer(0);
for (int64_t i = 0; i < vertices->getNumberOfVertices(); i++)
{
verts[3 * i] = float(0.1 + i);
verts[3 * i + 1] = float(0.2 + i);
verts[3 * i + 2] = float(0.3 + i);
}
m->setGeometry(vertices);
}
void checkPoints(size_t start, size_t end) const
{
float radius = 0.0f;
FloatArrayType::Pointer llPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Lower_Left");
FloatArrayType::Pointer urPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Upper_Right");
FloatArrayType::Pointer ll_rotPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Lower_Left_Rotated");
FloatArrayType::Pointer ur_rotPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Upper_Right_Rotated");
float* ll = llPtr->getPointer(0);
float* ur = urPtr->getPointer(0);
float* ll_rot = ll_rotPtr->getPointer(0);
float* ur_rot = ur_rotPtr->getPointer(0);
float* point = NULL;
char code = ' ';
float g[3][3] = { { 0.0f, 0.0f, 0.0f }, { 0.0f, 0.0f, 0.0f } };
for (size_t iter = start; iter < end; iter++)
{
Int32Int32DynamicListArray::ElementList& faceIds = m_FaceIds->getElementList(iter);
FOrientArrayType om(9, 0.0);
FOrientTransformsType::qu2om(FOrientArrayType(m_AvgQuats[iter]), om);
om.toGMatrix(g);
// find bounding box for current feature
GeometryMath::FindBoundingBoxOfFaces(m_Faces, faceIds, ll, ur);
GeometryMath::FindBoundingBoxOfRotatedFaces(m_Faces, faceIds, g, ll_rot, ur_rot);
GeometryMath::FindDistanceBetweenPoints(ll, ur, radius);
generatePoints(iter, m_Points, m_InFeature, m_AvgQuats, m_LatticeConstants, m_Basis, ll_rot, ur_rot);
// check points in vertex array to see if they are in the bounding box of the feature
int64_t numPoints = m_Points[iter]->getNumberOfVertices();
VertexGeom::Pointer vertArray = m_Points[iter];
BoolArrayType::Pointer boolArray = m_InFeature[iter];
for (int64_t i = 0; i < numPoints; i++)
{
point = vertArray->getVertexPointer(i);
if (boolArray->getValue(i) == false)
{
code = GeometryMath::PointInPolyhedron(m_Faces, faceIds, m_FaceBBs, point, ll, ur, radius);
if (code == 'i' || code == 'V' || code == 'E' || code == 'F') { m_InFeature[start]->setValue(i, true); }
}
}
}
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::assign_points(QVector<VertexGeom::Pointer> points, QVector<BoolArrayType::Pointer> inFeature)
{
size_t count = 0;
int32_t numFeatures = points.size();
for (int32_t i = 0; i < numFeatures; i++)
{
int64_t numPoints = points[i]->getNumberOfVertices();
bool* inside = inFeature[i]->getPointer(0);
for (int64_t j = 0; j < numPoints; j++)
{
if (inside[j] == true) { count++; }
}
}
DataContainer::Pointer v = getDataContainerArray()->getDataContainer(getVertexDataContainerName());
VertexGeom::Pointer vertices = VertexGeom::CreateGeometry(count, DREAM3D::VertexData::SurfaceMeshNodes);
AttributeMatrix::Pointer vertexAttrMat = v->getAttributeMatrix(getVertexAttributeMatrixName());
QVector<size_t> tDims(1, count);
vertexAttrMat->resizeAttributeArrays(tDims);
updateVertexInstancePointers();
count = 0;
float coords[3] = { 0.0f, 0.0f, 0.0f };
for (int32_t i = 0; i < numFeatures; i++)
{
int64_t numPoints = points[i]->getNumberOfVertices();
bool* inside = inFeature[i]->getPointer(0);
for (int64_t j = 0; j < numPoints; j++)
{
if (inside[j] == true)
{
coords[0] = points[i]->getVertexPointer(j)[0];
coords[1] = points[i]->getVertexPointer(j)[1];
coords[2] = points[i]->getVertexPointer(j)[2];
vertices->setCoords(count, coords);
m_AtomFeatureLabels[count] = i;
count++;
}
}
}
v->setGeometry(vertices);
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void MakeDataContainer::execute()
{
int err = 0;
setErrorCondition(err);
// Run the data check to get references to all of our data arrays initialized to the values stored in memory
dataCheck();
if (getErrorCondition() < 0)
{
return;
}
//ImageGeom::Pointer image = getDataContainerArray()->getDataContainer(getDataContainerName())->getGeometryAs<ImageGeom>();
//size_t index;
//size_t iDims[3] = {0, 0, 0};
//image->getDimensions(iDims);
//for (size_t z=0;z<image->getZPoints();z++)
//{
// for (size_t y=0;y<image->getYPoints();y++)
// {
// for (size_t x=0;x<image->getXPoints();x++)
// {
// index = (z * iDims[0] * iDims[1]) + (y * iDims[0]) + x;
// m_FeatureIds[index] = z + x + y;
// }
// }
//}
VertexGeom::Pointer verts = getDataContainerArray()->getDataContainer(getDataContainerName())->getGeometryAs<VertexGeom>();
for (int64_t i = 0; i < verts->getNumberOfVertices(); i++)
{
m_FeatureIds[i] = i;
}
/* Let the GUI know we are done with this filter */
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
VertexGeom::Pointer RegularGridSampleSurfaceMesh::generate_points()
{
VertexGeom::Pointer points = VertexGeom::CreateGeometry((m_XPoints * m_YPoints * m_ZPoints), "_INTERNAL_USE_ONLY_points");
int64_t count = 0;
float coords[3] = { 0.0f, 0.0f, 0.0f };
for (int64_t k = 0; k < m_ZPoints; k++)
{
for (int64_t j = 0; j < m_YPoints; j++)
{
for (int64_t i = 0; i < m_XPoints; i++)
{
coords[0] = (float(i) + 0.5f) * m_Resolution.x + m_Origin.x;
coords[1] = (float(j) + 0.5f) * m_Resolution.y + m_Origin.y;
coords[2] = (float(k) + 0.5f) * m_Resolution.z + m_Origin.z;
points->setCoords(count, coords);
count++;
}
}
}
return points;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void InsertAtoms::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
// Validate that the selected AvgQuats array has tuples equal to the largest
// Feature Id; the filter would not crash otherwise, but the user should
// be notified of unanticipated behavior ; this cannot be done in the dataCheck since
// we don't have acces to the data yet
int32_t numFeaturesIn = static_cast<int32_t>(m_AvgQuatsPtr.lock()->getNumberOfTuples());
bool mismatchedFeatures = true;
int32_t largestFeature = 0;
size_t numTuples = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();
for (size_t i = 0; i < numTuples; i++)
{
if (m_SurfaceMeshFaceLabels[2 * i] > largestFeature)
{
largestFeature = m_SurfaceMeshFaceLabels[2 * i];
if (largestFeature >= numFeaturesIn)
{
mismatchedFeatures = true;
break;
}
}
else if (m_SurfaceMeshFaceLabels[2 * i + 1] > largestFeature)
{
largestFeature = m_SurfaceMeshFaceLabels[2 * i + 1];
if (largestFeature >= numFeaturesIn)
{
mismatchedFeatures = true;
break;
}
}
}
if (mismatchedFeatures == true)
{
QString ss = QObject::tr("The number of Features in the AvgQuats array (%1) is larger than the largest Feature Id in the SurfaceMeshFaceLabels array").arg(numFeaturesIn);
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
if (largestFeature != (numFeaturesIn - 1))
{
QString ss = QObject::tr("The number of Features in the AvgQuats array (%1) does not match the largest Feature Id in the SurfaceMeshFaceLabels array").arg(numFeaturesIn);
setErrorCondition(-5555);
notifyErrorMessage(getHumanLabel(), ss, getErrorCondition());
return;
}
FloatVec3_t latticeConstants;
latticeConstants.x = m_LatticeConstants.x / 10000.0;
latticeConstants.y = m_LatticeConstants.y / 10000.0;
latticeConstants.z = m_LatticeConstants.z / 10000.0;
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(getSurfaceMeshFaceLabelsArrayPath().getDataContainerName());
SIMPL_RANDOMNG_NEW()
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
bool doParallel = true;
#endif
// pull down faces
TriangleGeom::Pointer triangleGeom = sm->getGeometryAs<TriangleGeom>();
int64_t numFaces = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();
// create array to hold bounding vertices for each face
FloatArrayType::Pointer llPtr = FloatArrayType::CreateArray(3, "Lower_Left_Internal_Use_Only");
FloatArrayType::Pointer urPtr = FloatArrayType::CreateArray(3, "Upper_Right_Internal_Use_Only");
float* ll = llPtr->getPointer(0);
float* ur = urPtr->getPointer(0);
VertexGeom::Pointer faceBBs = VertexGeom::CreateGeometry(2 * numFaces, "faceBBs");
// walk through faces to see how many features there are
int32_t g1 = 0, g2 = 0;
int32_t maxFeatureId = 0;
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > maxFeatureId) { maxFeatureId = g1; }
if (g2 > maxFeatureId) { maxFeatureId = g2; }
}
// add one to account for feature 0
int32_t numFeatures = maxFeatureId + 1;
// create a dynamic list array to hold face lists
Int32Int32DynamicListArray::Pointer faceLists = Int32Int32DynamicListArray::New();
QVector<int32_t> linkCount(numFeatures, 0);
// fill out lists with number of references to cells
typedef boost::shared_array<int32_t> SharedInt32Array_t;
SharedInt32Array_t linkLocPtr(new int32_t[numFaces]);
int32_t* linkLoc = linkLocPtr.get();
::memset(linkLoc, 0, numFaces * sizeof(int32_t));
// traverse data to determine number of faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { linkCount[g1]++; }
if (g2 > 0) { linkCount[g2]++; }
}
// now allocate storage for the faces
faceLists->allocateLists(linkCount);
// traverse data again to get the faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { faceLists->insertCellReference(g1, (linkLoc[g1])++, i); }
if (g2 > 0) { faceLists->insertCellReference(g2, (linkLoc[g2])++, i); }
// find bounding box for each face
GeometryMath::FindBoundingBoxOfFace(triangleGeom, i, ll, ur);
faceBBs->setCoords(2 * i, ll);
faceBBs->setCoords(2 * i + 1, ur);
}
// generate the list of sampling points fom subclass
QVector<VertexGeom::Pointer> points(numFeatures);
QVector<BoolArrayType::Pointer> inFeature(numFeatures);
for (int32_t i = 0; i < numFeatures; i++)
{
points[i] = VertexGeom::CreateGeometry(0, "_INTERNAL_USE_ONLY_points");
inFeature[i] = BoolArrayType::CreateArray(0, "_INTERNAL_USE_ONLY_inside");
}
QuatF* avgQuats = reinterpret_cast<QuatF*>(m_AvgQuats);
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, numFeatures),
InsertAtomsImpl(triangleGeom, faceLists, faceBBs, avgQuats, latticeConstants, m_Basis, points, inFeature), tbb::auto_partitioner());
}
else
#endif
{
InsertAtomsImpl serial(triangleGeom, faceLists, faceBBs, avgQuats, latticeConstants, m_Basis, points, inFeature);
serial.checkPoints(0, numFeatures);
}
assign_points(points, inFeature);
notifyStatusMessage(getHumanLabel(), "Complete");
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
int DataContainer::readMeshDataFromHDF5(hid_t dcGid, bool preflight)
{
herr_t err = 0;
unsigned int geometryType = DREAM3D::GeometryType::UnknownGeometry;
err = QH5Lite::readScalarAttribute(dcGid, DREAM3D::Geometry::Geometry, DREAM3D::Geometry::GeometryType, geometryType);
if (err < 0)
{
return err;
}
hid_t geometryId = H5Gopen(dcGid, DREAM3D::Geometry::Geometry.toLatin1().data(), H5P_DEFAULT);
if (geometryId < 0)
{
return -1;
}
HDF5ScopedGroupSentinel gSentinel(&geometryId, false);
IGeometry::Pointer geomPtr = IGeometry::NullPointer();
if (NULL == m_Geometry.get())
{
switch(geometryType)
{
case DREAM3D::GeometryType::ImageGeometry:
{
ImageGeom::Pointer image = ImageGeom::New();
err = image->readGeometryFromHDF5(geometryId, preflight);
err = GeometryHelpers::GeomIO::ReadMetaDataFromHDF5(dcGid, image);
setGeometry(image);
break;
}
case DREAM3D::GeometryType::VertexGeometry:
{
VertexGeom::Pointer vertices = VertexGeom::New();
err = vertices->readGeometryFromHDF5(geometryId, preflight);
err = GeometryHelpers::GeomIO::ReadMetaDataFromHDF5(dcGid, vertices);
setGeometry(vertices);
break;
}
case DREAM3D::GeometryType::EdgeGeometry:
{
EdgeGeom::Pointer edges = EdgeGeom::New();
err = edges->readGeometryFromHDF5(geometryId, preflight);
err = GeometryHelpers::GeomIO::ReadMetaDataFromHDF5(dcGid, edges);
setGeometry(edges);
break;
}
case DREAM3D::GeometryType::TriangleGeometry:
{
TriangleGeom::Pointer triangles = TriangleGeom::New();
err = triangles->readGeometryFromHDF5(geometryId, preflight);
err = GeometryHelpers::GeomIO::ReadMetaDataFromHDF5(dcGid, triangles);
setGeometry(triangles);
break;
}
case DREAM3D::GeometryType::QuadGeometry:
{
QuadGeom::Pointer quads = QuadGeom::New();
err = quads->readGeometryFromHDF5(geometryId, preflight);
err = GeometryHelpers::GeomIO::ReadMetaDataFromHDF5(dcGid, quads);
setGeometry(quads);
break;
}
case DREAM3D::GeometryType::UnknownGeometry:
setGeometry(geomPtr);
break;
default:
setGeometry(geomPtr);
break;
}
}
return err;
}
// -----------------------------------------------------------------------------
//
// -----------------------------------------------------------------------------
void SampleSurfaceMesh::execute()
{
setErrorCondition(0);
dataCheck();
if(getErrorCondition() < 0) { return; }
DataContainer::Pointer sm = getDataContainerArray()->getDataContainer(m_SurfaceMeshFaceLabelsArrayPath.getDataContainerName());
SIMPL_RANDOMNG_NEW()
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
bool doParallel = true;
#endif
TriangleGeom::Pointer triangleGeom = sm->getGeometryAs<TriangleGeom>();
// pull down faces
int64_t numFaces = m_SurfaceMeshFaceLabelsPtr.lock()->getNumberOfTuples();
// create array to hold bounding vertices for each face
FloatArrayType::Pointer llPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Lower_Left");
FloatArrayType::Pointer urPtr = FloatArrayType::CreateArray(3, "_INTERNAL_USE_ONLY_Upper_Right");
float* ll = llPtr->getPointer(0);
float* ur = urPtr->getPointer(0);
VertexGeom::Pointer faceBBs = VertexGeom::CreateGeometry(2 * numFaces, "_INTERNAL_USE_ONLY_faceBBs");
// walk through faces to see how many features there are
int32_t g1 = 0, g2 = 0;
int32_t maxFeatureId = 0;
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > maxFeatureId) { maxFeatureId = g1; }
if (g2 > maxFeatureId) { maxFeatureId = g2; }
}
// add one to account for feature 0
int32_t numFeatures = maxFeatureId + 1;
// create a dynamic list array to hold face lists
Int32Int32DynamicListArray::Pointer faceLists = Int32Int32DynamicListArray::New();
std::vector<int32_t> linkCount(numFeatures, 0);
// fill out lists with number of references to cells
typedef boost::shared_array<int32_t> SharedInt32Array_t;
SharedInt32Array_t linkLocPtr(new int32_t[numFaces]);
int32_t* linkLoc = linkLocPtr.get();
::memset(linkLoc, 0, numFaces * sizeof(int32_t));
// traverse data to determine number of faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { linkCount[g1]++; }
if (g2 > 0) { linkCount[g2]++; }
}
// now allocate storage for the faces
faceLists->allocateLists(linkCount);
// traverse data again to get the faces belonging to each feature
for (int64_t i = 0; i < numFaces; i++)
{
g1 = m_SurfaceMeshFaceLabels[2 * i];
g2 = m_SurfaceMeshFaceLabels[2 * i + 1];
if (g1 > 0) { faceLists->insertCellReference(g1, (linkLoc[g1])++, i); }
if (g2 > 0) { faceLists->insertCellReference(g2, (linkLoc[g2])++, i); }
// find bounding box for each face
GeometryMath::FindBoundingBoxOfFace(triangleGeom, i, ll, ur);
faceBBs->setCoords(2 * i, ll);
faceBBs->setCoords(2 * i + 1, ur);
}
// generate the list of sampling points from subclass
VertexGeom::Pointer points = generate_points();
if(getErrorCondition() < 0 || NULL == points.get()) { return; }
int64_t numPoints = points->getNumberOfVertices();
// create array to hold which polyhedron (feature) each point falls in
Int32ArrayType::Pointer iArray = Int32ArrayType::NullPointer();
iArray = Int32ArrayType::CreateArray(numPoints, "_INTERNAL_USE_ONLY_polyhedronIds");
iArray->initializeWithZeros();
int32_t* polyIds = iArray->getPointer(0);
#ifdef SIMPLib_USE_PARALLEL_ALGORITHMS
if (doParallel == true)
{
tbb::parallel_for(tbb::blocked_range<size_t>(0, numFeatures),
SampleSurfaceMeshImpl(triangleGeom, faceLists, faceBBs, points, polyIds), tbb::auto_partitioner());
}
else
#endif
{
SampleSurfaceMeshImpl serial(triangleGeom, faceLists, faceBBs, points, polyIds);
serial.checkPoints(0, numFeatures);
}
assign_points(iArray);
notifyStatusMessage(getHumanLabel(), "Complete");
}